Ubiquitin ligase NEDD4 promotes the proliferation of hepatocellular carcinoma cells through targeting PCDH17 protein for ubiquitination and degradation.

Neural precursor cell expressed developmentally downregulated 4 (NEDD4), an E3 ubiquitin ligase, is commonly upregulated in human hepatocellular carcinoma (HCC) and functions as an oncogenic factor in the progression of HCC, but the molecular mechanism needs be further explored. In this study, we found that NEDD4 could facilitate the proliferation of HCC cells, which was associated with regulating the ERK signaling. Further investigation showed that protocadherin 17 (PCDH17) was a potential substrate of NEDD4, and restoration of PCDH17 could block the facilitation of ERK signaling and HCC cells proliferation induced by NEDD4 overexpression. Whereafter, we confirmed that NEDD4 interacted with PCDH17 and promoted the Lys33-linked polyubiquitination and degradation of it via the proteasome pathway. Finally, NEDD4 protein level was found to be inversely correlated with that of PCDH17 in human HCC tissues. In conclusion, these results suggest that NEDD4 acts as an E3 ubiquitin ligase for PCDH17 ubiquitination and degradation thereby promoting the proliferation of HCC cells through regulating the ERK signaling, which may provide novel evidence for NEDD4 to be a promising therapeutic target for HCC.

SIAH2 suppresses c-JUN pathway by promoting the polyubiquitination and degradation of HBx in hepatocellular carcinoma.

As an important protein encoded by hepatitis B virus (HBV), HBV X protein (HBx) plays an important role in the development of hepatocellular carcinoma (HCC). It has been shown that seven in absentia homologue 1 (SIAH1) could regulates the degradation of HBx through the ubiquitin-proteasome pathway. However, as a member of SIAH family, the regulatory effects of SIAH2 on HBx remain unclear. In this study, we first confirmed that SIAH2 could reduce the protein levels of HBx depending on its E3 ligase activity. Moreover, SIAH2 interacted with HBx and induced its K48-linked polyubiquitination and proteasomal degradation. Furthermore, we provided evidence that SIAH2 inhibits HBx-associated HCC cells proliferation by regulating HBx. In conclusion, our study identified a novel role for SIAH2 in promoting HBx degradation and SIAH2 exerts an inhibitory effect in the proliferation of HBx-associated HCC through inducing the degradation of HBx. Our study provides a new idea for the targeted degradation of HBx and may have great huge significance into providing novel evidence for the targeted therapy of HBV-infected HCC.

Long range topography by dispersion unmatched spectral-domain interferometry based on virtually imaged phased array modes.

We propose to realize a long range topography by dispersion unmatched spectral-domain interferometry based on virtually imaged phased array (VIPA) modes. By filtering the continuous spectrum of a supercontinuum source through a side-entrance Fabry-Perot etalon configured at two input angles, two groups of VIPA modes are generated. A method based on unmatched dispersion is proposed for non-aliasing reconstruction of the true depth from the interference spectrum under-sampled at two groups of VIPA modes. With the high spectral resolution provided by the VIPA modes instead of the grating-based spectrometer, only a 10 dB falloff in sensitivity over a range of 10 mm was demonstrated. The feasibility of the proposed method was confirmed by topography of a sample of gauge blocks and a model of three-dimensional (3D) printed tooth. The occlusal surface of the tooth model was further quantitatively evaluated, demonstrating its potential application in long range 3D topography.

SIAH1/CTR9 axis promotes the epithelial-mesenchymal transition of hepatocellular carcinoma.

SIAH1 has been reported to participate in several human cancers, including hepatocellular carcinoma (HCC). However, the effect of SIAH1 on the epithelial-mesenchymal transition (EMT) has not been reported in HCC cells. Here, we discovered the inhibitory effect of SIAH1 on HCC cell migration and invasion, which was related with regulating EMT. Molecularly, a yeast two-hybrid experiment indicated that Cln Three Requiring 9 (CTR9) was a potential interacting protein of SIAH1, which was further verified by co-immunoprecipitation assays. Furthermore, SIAH1 inhibited the EMT of HCC cells through negatively regulating CTR9. Importantly, CTR9 was ubiquitinated and degraded by SIAH1 via the proteasome pathway in HCC cells. Additionally, it was showed that SIAH1 mainly mediated the K48-linked polyubiquitination on CTR9. Finally, the protein level of CTR9 was found to be inversely correlated with SIAH1 in human HCC tissues. Summed up all together, these findings reveal that SIAH1/CTR9 axis promotes the EMT of HCC cells and is a promising therapeutic target for HCC therapy.

MALAT1 knockdown alleviates the pyroptosis of microglias in diabetic cerebral ischemia via regulating STAT1 mediated NLRP3 transcription.

BACKGROUND: Dysregulated long non-coding RNAs participate in the development of diabetic cerebral ischemia. This study aimed to investigate the underlying mechanism of lncRNA MALAT1 in diabetic cerebral ischemia. METHOD: Middle cerebral artery occlusion (MCAO) was performed to establish diabetic cerebral I/R in vivo. TTC and neurological deficits assessment were performed to assess cerebral ischemic injury. LDH was conducted to detect cytotoxicity. RT-qPCR and western blotting assays were applied to determine mRNA and protein expression. Flow cytometry was performed to detect the pyroptosis of BV2 cells. Immunofluorescence and FISH were conducted for subcellular localization of MALAT1 and STAT1. ELISA was performed to determine cytokine release. Dual luciferase reporter, RIP, and ChIP assays were used to validate the interaction between STAT1 and MALAT1/NLRP3. Diabetes aggravated cerebral injury in vivo and in vitro. Diabetic cerebral ischemia induced inflammatory response and inflammation-induced cell pyroptosis. RESULT: MALAT1 was overexpressed in diabetic cerebral ischemia models in vivo and in vitro. However, knockdown of MALAT1 suppressed inflammatory response and the pyroptosis of BV2 cells. Moreover, MALAT1 interacted with STAT1 to transcriptionally activate NLRP3. Knockdown of STAT1 significantly reversed the effects of MALAT1. Furthermore, STAT1 promotes the MALAT1 transcription. MALAT1 interacts with STAT1 to promote the pyroptosis of microglias induced by diabetic cerebral ischemia through activating NLRP3 transcription. CONCLUSION: Thus, knockdown of MALAT1 may be a potential promising therapy target for diabetic cerebral ischemia.

Optical reflection characteristic-based emissivity analysis of a pyramid array flat-plate blackbody for remote sensor calibration.

The flat-plate blackbody (FPB) is the core device in infrared remote sensing radiometric calibration for providing accurate infrared radiation energy. The emissivity of an FPB is an important parameter that directly affects calibration accuracy. This paper uses a pyramid array structure based on the regulated optical reflection characteristics to analyze the FPB's emissivity quantitatively. The analysis is accomplished by performing emissivity simulations based on the Monte Carlo method. The effects of specular reflection (SR), near-specular reflection (NSR), and diffuse reflection (DR) on the emissivity of an FPB with pyramid arrays are analyzed. In addition, various patterns of normal emissivity, small-angle directional emissivity, and emissivity uniformity are examined under different reflection characteristics. Further, the blackbodies with the NSR and DR are fabricated and tested experimentally. The experimental results show a good agreement with the corresponding simulation results. The emissivity of the FPB with the NSR can reach 0.996 in the 8-14 µm waveband. Finally, the emissivity uniformity of FPB samples at all tested positions and angles is better than 0.005 and 0.002, respectively. The standard uncertainty of experimental measurement of waveband emissivity and spectral emissivity are 0.47% and 0.38% respectively, and the simulation uncertainty is 0.10%.

Mapping port wine stain in vivo by optical coherence tomography angiography and multi-metric characterization.

Port wine stain (PWS) is a congenital cutaneous capillary malformation composed of ecstatic vessels, while the microstructure of these vessels remains largely unknown. Optical coherence tomography angiography (OCTA) serves as a non-invasive, label-free and high-resolution tool to visualize the 3D tissue microvasculature. However, even as the 3D vessel images of PWS become readily accessible, quantitative analysis algorithms for their organization have mainly remained limited to analysis of 2D images. Especially, 3D orientations of vasculature in PWS have not yet been resolved at a voxel-wise basis. In this study, we employed the inverse signal-to-noise ratio (iSNR)-decorrelation (D) OCTA (ID-OCTA) to acquire 3D blood vessel images in vivo from PWS patients, and used the mean-subtraction method for de-shadowing to correct the tail artifacts. We developed algorithms which mapped blood vessels in spatial-angular hyperspace in a 3D context, and obtained orientation-derived metrics including directional variance and waviness for the characterization of vessel alignment and crimping level, respectively. Combining with thickness and local density measures, our method served as a multi-parametric analysis platform which covered a variety of morphological and organizational characteristics at a voxel-wise basis. We found that blood vessels were thicker, denser and less aligned in lesion skin in contrast to normal skin (symmetrical parts of skin lesions on the cheek), and complementary insights from these metrics led to a classification accuracy of ∼90% in identifying PWS. An improvement in sensitivity of 3D analysis was validated over 2D analysis. Our imaging and analysis system provides a clear picture of the microstructure of blood vessels within PWS tissues, which leads to a better understanding of this capillary malformation disease and facilitates improvements in diagnosis and treatment of PWS.

Adsorption of sulfur-containing contaminant gases by pristine, Cr and Mo doped NbS2monolayers based on density functional theory.

The adsorption and sensor performance of hazardous gases containing sulfur (SO2, H2S and SO3) on pristine, Cr and Mo doped NbS2monolayers (Cr-NbS2and Mo-NbS2) were investigated in detail based on density functional theory. The comparative analysis of the parameters such as density of states, adsorption energy, charge transfer, recovery time and work function of the systems showed that the pristine NbS2monolayer have poor sensor performance for sulfur-containing hazardous gases due to weak adsorption capacity, insignificant charge transfer and insignificant changes in electronic properties after gas adsorption on the surface. After doping with Cr atoms, the adsorption performance of Cr-NbS2was significantly improved, and it can be used as a sensor for SO2and H2S gases and as an adsorbent for SO3gas. The adsorption performance of Mo-NbS2is also significantly improved by doping with Mo atoms, and it can be used as a sensor for H2S gas and as an adsorbent for SO2and SO3gas. Therefore, Cr-NbS2and Mo-NbS2are revealed to be sensing or elimination materials for the harmful gases containing sulfur (SO2, H2S and SO3) in the atmosphere.

Dexmedetomidine reduces enteric glial cell injury induced by intestinal ischaemia-reperfusion injury through mitochondrial localization of TERT.

This study was performed to uncover the effects of dexmedetomidine on oxidative stress injury induced by mitochondrial localization of telomerase reverse transcriptase (TERT) in enteric glial cells (EGCs) following intestinal ischaemia-reperfusion injury (IRI) in rat models. Following establishment of intestinal IRI models by superior mesenteric artery occlusion in Wistar rats, the expression and distribution patterns of TERT were detected. The IRI rats were subsequently treated with low or high doses of dexmedetomidine, followed by detection of ROS, MDA and GSH levels. Calcein cobalt and rhodamine 123 staining were also carried out to detect mitochondrial permeability transition pore (MPTP) and the mitochondrial membrane potential (MMP), respectively. Moreover, oxidative injury of mtDNA was determined, in addition to analyses of EGC viability and apoptosis. Intestinal tissues and mitochondria of EGCs were badly damaged in the intestinal IRI group. In addition, there was a reduction in mitochondrial localization of TERT, oxidative stress, whilst apoptosis of EGCs was increased and proliferation was decreased. On the other hand, administration of dexmedetomidine was associated with promotion of mitochondrial localization of TERT, whilst oxidative stress, MPTP and mtDNA in EGCs, and EGC apoptosis were all inhibited, and the MMP and EGC viability were both increased. A positive correlation was observed between different doses of dexmedetomidine and protective effects. Collectively, our findings highlighted the antioxidative effects of dexmedetomidine on EGCs following intestinal IRI, as dexmedetomidine alleviated mitochondrial damage by enhancing the mitochondrial localization of TERT.

Optimized number of the primary singular values for image reconstruction in reflection matrix based optical coherence tomography.

A reflection matrix based optical coherence tomography (OCT) is recently proposed and expected to extend the imaging-depth limit twice. However, the imaging depth and hence the image quality heavily depend on the number of primary singular values considered for image reconstruction. To this regard, we propose a method based on correlation between image pairs reconstructed from different number of singular values and corresponding remainders. The obtained correlation curve and another feature curve fetched from the former are then fed to a long short-term memory (LSTM) network classifier to identify the optimized number of primary singular values for image reconstruction. Simulated targets with different combinations of filling fraction and signal-to-noise ratio (SNR) are reconstructed by the developed method as well as two current adopted methods for comparison. The results demonstrate that the proposed method is robust to recover the image with satisfactory similarity close to the reference one. To our knowledge, this is the first comprehensive study on the optimized number of the primary singular values considered for image reconstruction in reflection matrix based OCT.

Identification of human ovarian cancer relying on collagen fiber coverage features by quantitative second harmonic generation imaging.

Ovarian cancer has the highest mortality rate among all gynecological cancers, containing complicated heterogeneous histotypes, each with different treatment plans and prognoses. The lack of screening test makes new perspectives for the biomarker of ovarian cancer of great significance. As the main component of extracellular matrix, collagen fibers undergo dynamic remodeling caused by neoplastic activity. Second harmonic generation (SHG) enables label-free, non-destructive imaging of collagen fibers with submicron resolution and deep sectioning. In this study, we developed a new metric named local coverage to quantify morphologically localized distribution of collagen fibers and combined it with overall density to characterize 3D SHG images of collagen fibers from normal, benign and malignant human ovarian biopsies. An overall diagnosis accuracy of 96.3% in distinguishing these tissue types made local and overall density signatures a sensitive biomarker of tumor progression. Quantitative, multi-parametric SHG imaging might serve as a potential screening test tool for ovarian cancer.

Identification of endoplasmic reticulum formation mechanism by multi-parametric, quantitative super-resolution imaging.

The endoplasmic reticulum (ER) is a highly dynamic membrane-bound organelle in eukaryotic cells which spreads throughout the whole cell and contacts and interacts with almost all organelles, yet quantitative approaches to assess ER reorganization are lacking. Herein we propose a multi-parametric, quantitative method combining pixel-wise orientation and waviness features and apply it to the time-dependent images of co-labeled ER and microtubule (MT) from U2OS cells acquired from two-dimensional structured illumination microscopy (2D SIM). Analysis results demonstrate that these morphological features are sensitive to ER reshaping and a combined use of them is a potential biomarker for ER formation. A new, to the best of our knowledge, mechanism of MT-associated ER formation, termed hooking, is identified based on distinct organizational alterations caused by interaction between ER and MT which are different from those of the other three mechanisms already known, validated by 100% discrimination accuracy in classifying four MT-associated ER formation mechanisms.

Aloe polysaccharide promotes osteogenesis potential of adipose-derived stromal cells via BMP-2/Smads and prevents ovariectomized-induced osteoporosis.

BACKGROUND: Aloe polysaccharide (AP) is a type of an active macromolecule of Aloe vera, which contributes to its function. However, whether AP possesses anti-osteoporosis properties is unknown. METHODS: Adipose-derived stromal cells were treated with different concentrations of AP. Early and late osteogenesis were, respectively, evaluated by ALP and Alizarin Red S staining. The effect of AP on the processes of adipogenesis inhibition in ADSCs was analyzed by oil red O staining. Western blot was used to assess the expression of osteogenic and adipogenic related factors. Then, Noggin was administered to further confirm the mechanism by which AP promotes the osteogenesis of ADSCs. Finally, 40 female SD rats were classified into a bilateral laparotomy group (Sham group) and three bilateral ovariectomy groups: OVX group, OVX + AP group, and OVX + AP + Noggin group. The bilateral rat femurs were collected to perform micro-CT scanning, HE, Masson trichrome, and Oil red O staining. RESULTS: The results indicated that AP could increase ALP expression and calcium deposition. Through molecular mechanisms, AP promotes the protein expression of COL1A1, OPN, and ALP in ADSCs, but downregulates the expression of PPARγ. Also, AP directs ADSCs' fate by stimulating the BMP2/Smads signaling pathway. In vivo, the rat AP-treated had more trabecular bone than the OVX rat, indicating partial protection from cancellous bone loss after treatment with AP. CONCLUSION: Our results show that AP may promote osteogenesis of ADSCs through BMP-2/Smads signaling pathway and inhibits lipogenic differentiation. Thus, AP might be a promising alternative medicine to treat postmenopausal osteoporosis.

Transcriptional regulator CTR9 promotes hepatocellular carcinoma progression and metastasis via increasing PEG10 transcriptional activity.

Cln Three Requiring 9 (CTR9), a scaffold protein of the polymerase-associated factor-1 (PAF1) complex (PAF1c), is primarily localized in the nucleus of cells. Recent studies show that CTR9 plays essential roles in the development of various human cancers and their occurrence; however, its regulatory roles and precise mechanisms in hepatocellular carcinoma (HCC) remain unclear. In this study, we investigated the roles of CTR9 using in vitro assays and a xenograft mouse model. We found that CTR9 protein is upregulated in tumor tissues from HCC patients. Knockdown of CTR9 substantially reduced HCC cell proliferation, invasion, and migration, whereas its overexpression promoted these activities. In addition, in vitro results revealed that CTR9 silencing dramatically increased cell cycle regulators, p21 and p27, but markedly decreased matrix metalloproteinases, MMP2 and MMP9, with these outcomes reversed upon CTR9 overexpression. Furthermore, the underlying molecular mechanism suggests that CTR9 promoted the oncogene paternally expressed gene 10 (PEG10) transcription via its promoter region. Finally, the oncogenic roles of CTR9 were confirmed in a xenograft mouse model. This study confirms that CTR9, an oncoprotein that promotes HCC cell proliferation, invasion, and migration, increases tumor growth in a xenograft mouse model. CTR9 could be a novel therapeutic target. Further investigation is warranted to verify CTR9 potential in novel therapies for HCC.

Chemical composition, sources and optical properties of nitrated aromatic compounds in fine particulate matter during winter foggy days in Nanjing, China.

Functionalized aromatic compounds are one of the most important light-absorbing organic chromophores - so-called brown carbon (BrC) - in fine particulate matter (PM2.5). In this study, we conducted a wintertime field campaign to measure eight nitrated aromatic compounds (NACs) in PM2.5 with offline analysis techniques, including liquid chromatograph mass spectrometer (LC-MS) and aerodyne high-resolution aerosol mass spectrometer (AMS) measurements, during foggy and nonfoggy days in suburban Nanjing in the Yangtze River Delta region, China. On average, 4-nitrophenol could be one of the most important light absorbing materials in the observed BrC, which accounted for over 40% of the mass concentration of identified chromophores. The mass concentration of 2-methyl-4-nitrophenol and 2,6-dimethyl-4-nitrophenol were evidently increased during foggy days, contribution of which to total NACs were increased by 10% and 5%, respectively. Positive matrix factorization analysis of combining LC-MS and AMS dataset was performed to identify the primary and secondary sources of NACs. Primary sources, e.g., traffic and solid-fuel combustion, accounted for 71% of the sum of 4-nitrophenol, 2,6-dimethyl-4-nitrophenol and 3-nitrosalicylic acid, suggesting important contribution of primary emissions to these NACs. The contribution of secondary sources, associated with two oxygenated organic aerosols, could contribute 66% to 4-nitrophenol, reflecting the link of such nitrated aromatic compounds to secondary organic aerosol source. Together with optical measurements, 4-nitrophenol presented a high contribution (>50%) to the identified BrC absorbance in the light range 250 and 550 nm was observed. This could highlight an important role of such NACs in ambient BrC light absorption, despite its mass contribution to total organic carbon was negligible. Our work could improve the understanding of the links between optical properties and chemical composition of BrC, and the difference between BrC chromophores from nonfoggy days and foggy days under the typical polluted atmospheric conditions.

Particulate organic nitrates at Mount Tai in winter and spring: Variation characteristics and effects of mountain-valley breezes and elevated emission sources.

Particulate organic nitrates, among the major components of secondary organic aerosols and fine particles, play important roles in regional nitrogen cycle, ozone budget, and cloud condensation nuclei formation. However, the pollution characteristics of particulate organic nitrates at mountain areas and the effects of anthropogenic pollutant transport remain poorly understood. In this study, field sampling and measurements were conducted at a high-elevation mountain site over North China Plain in winter and spring. Total five kinds of particulate organic nitrates in fine particles were determined by ultra-high performance liquid chromatography-electrospray mass spectrometry. The average total concentrations of particulate organic nitrates were 330 ± 121 ng m-3 and 247 ± 63 ng m-3 in winter and spring. The monoterpene-derived organic nitrates were the dominant components in both seasons with their contribution higher than 70%, accounting for 1.2 ± 0.8% and 2.0 ± 1.0% in organic aerosols in winter and spring, respectively. The significantly higher levels of particulate organic nitrates in winter than spring was ascribed to the strong effects of mountain-valley breezes and coal combustion plumes. The increasing concentrations of NOx and particulate matters brought by the valley breeze at daytime facilitated the formation of MHN215, OAKN359, and OAHN361, while the rising SO2 abundance and the sulfate aerosols transported by elevated emission sources affected the formation of MDCN247 at nighttime.

Production Review of Accelerator-Based Medical Isotopes.

The production of reactor-based medical isotopes is fragile, which has meant supply shortages from time to time. This paper reviews alternative production methods in the form of cyclotrons, linear accelerators and neutron generators. Finally, the status of the production of medical isotopes in China is described.

ANP32A promotes the proliferation, migration and invasion of hepatocellular carcinoma by modulating the HMGA1/STAT3 pathway.

Acidic leucine-rich nuclear phosphoprotein-32A (ANP32A) has been reported to play an essential role in the development and progression of various human cancers. However, its expression pattern and possible mechanism in human hepatocellular carcinoma (HCC) remain to be elucidated. In this study, we used western blot and immunohistochemical staining to detect protein expression. The effects of ANP32A on the proliferation, migration and invasion of HCC cells were examined using 5-ethynyl-20-deoxyuridine (EdU), colony formation, CCK-8, and transwell assays. RT-qPCR was performed to detect mRNA expression. The interaction between ANP32A and the high mobility group A1 (HMGA1) mRNA was assessed using RNA immunoprecipitation (RIP). The tumorigenicity of ANP32A was assessed by establishing a xenograft tumor model in Balb/c nude mice. We found that the ANP32A protein was expressed at high levels in patients with HCC, which was associated with a poor prognosis. Functional experiments revealed that the silencing of ANP32A inhibited the proliferation, migration, and invasion of HCC cells, whereas overexpression of ANP32A promoted these processes. Further investigations indicated that ANP32A bound the HMGA1 mRNA and maintained its stability to promote the expression of HMGA1, thereby increasing the expression and activation of STAT3. Finally, a xenograft tumor model of Balb/c nude mice confirmed the tumorigenicity of ANP32A. This study found that ANP32A is up-regulated in patients with HCC and may accelerate the proliferation, migration and invasion of HCC cells by modulating the HMGA1/STAT3 pathway.

Dexmedetomidine inhibits mitochondria damage and apoptosis of enteric glial cells in experimental intestinal ischemia/reperfusion injury via SIRT3-dependent PINK1/HDAC3/p53 pathway.

BACKGROUND: Intestinal ischemia/reperfusion (I/R) injury commonly occurs during perioperative periods, resulting in high morbidity and mortality on a global scale. Dexmedetomidine (Dex) is a selective α2-agonist that is frequently applied during perioperative periods for its analgesia effect; however, its ability to provide protection against intestinal I/R injury and underlying molecular mechanisms remain unclear. METHODS: To fill this gap, the protection of Dex against I/R injury was examined in a rat model of intestinal I/R injury and in an inflammation cell model, which was induced by tumor necrosis factor-alpha (TNF-α) plus interferon-gamma (IFN-γ) stimulation. RESULTS: Our data demonstrated that Dex had protective effects against intestinal I/R injury in rats. Dex was also found to promote mitophagy and inhibit apoptosis of enteric glial cells (EGCs) in the inflammation cell model. PINK1 downregulated p53 expression by promoting the phosphorylation of HDAC3. Further studies revealed that Dex provided protection against experimentally induced intestinal I/R injury in rats, while enhancing mitophagy, and suppressing apoptosis of EGCs through SIRT3-mediated PINK1/HDAC3/p53 pathway in the inflammation cell model. CONCLUSION: Hence, these findings provide evidence supporting the protective effect of Dex against intestinal I/R injury and its underlying mechanism involving the SIRT3/PINK1/HDAC3/p53 axis.

Fast simulation and design of the fiber probe with a fiber-based pupil filter for optical coherence tomography using the eigenmode expansion approach.

Fiber probes for optical coherence tomography (OCT) recently employ a short section of step-index multimode fiber (SIMMF) to generate output beams with extended depth of focus (DOF). As the focusing region of the output beam is generally close to the probe end, it is not feasible to adopt the methods for bulk-optics with spatial pupil filters to the fiber probes with fiber-based filters. On the other hand, the applicable method of the beam propagation method (BPM) to the fiber probes is computationally inefficient to perform parameter scan and exhaustive search optimization. In this paper, we propose the method which analyzes the non-Gaussian beams from the fiber probes with fiber-based filters using the eigenmode expansion (EME) method. Furthermore, we confirm the power of this method in designing fiber-based filters with increased DOF gain and uniformly focusing by introducing more and higher-order fiber modes. These results using the EME method are in good agreement with that by the BPM, while the latter takes 1-2 orders more computation time. With higher-order fiber modes involved, a novel probe design with increased DOF gain and suppressed sidelobe is proposed. Our findings reveal that the fiber probes based on SIMMFs are able to achieve about four times DOF gain at maximum with uniformly focusing under acceptable modal dispersion. The EME method enables fast and accurate simulation of fiber probes based on SIMMFs, which is important in the design of high-performance fiber-based micro-imaging systems for biomedical applications.